Mike Mansfield, a CIA spokesman, said "the agency would take seriously, and follow up on, any allegations of impropriety", the Reuters news agency reported.
Robert Wood, a US state department spokesman, said the US "takes very seriously any accusations of misconduct involving any US personnel abroad".
"The individual in question has returned to Washington and the US government is looking into the matter," he said in statement quoted by Reuters.
The allegations could deal another major blow to the US image abroad at a time when Barack Obama, the US president, has called for improved relations with the Muslim world.
The first alleged victim reportedly said she was raped by the CIA officer in September 2007 after being invited to a party at his home by US embassy workers.
Later in the evening, she felt ill and woke up the next morning naked after being apparently raped, ABC News reported.
She said she had no recollection of having sex, the report says.
The second alleged victim described a similar incident that occurred in February 2008, the report said.
The man told investigators that he had engaged in consensual sex with the women, ABC News reported.
Drugs commonly used to intoxicate rape victims in such cases and about a dozen videotapes showing the man engaged in sexual acts were found when the officer's residence was searched, reports said.